It should be noted here that we obtained the curves in Fig. REF  from four BD simulation trajectories using the dWLC method, and each of the trajectories requires several weeks of CPU time. The calculation of the electrostatics interaction between the charged points on segments of the dWLC model indeed dominates the computational cost (see Text S6). According to our analyses, the computational cost of the dWLC in the plectonemic phase is still significant and grows linearly with the contour-length. For example, in Fig. REF , simulating a stretched DNA of 3000 \(bp\)  in 10 \(ms\)  costs 3 hours while simulating a pure plectoneme of the same contour length costs one day(i.e., the CPU time). The two-phase dynamic model, however, enables us to reduce the computational cost to trivial by dealing only with the essential variables with slow dynamics. In Fig. REF , the torque and extension curves generated from the two-phase dynamic model (using tens of seconds of computation time) well reproduce those in Fig.3(b) from the dWLC method and also consistent with previous experimental and computational studies[1]}, [2]}.
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